Cervical cancer, caused by Human Papillomavirus (HPV), is a global burden affecting women. The vaginal microbiome is associated with female reproductive health. Immuno-compromised HIV infected women are susceptible to persistent HPV infections. This study sought to characterize the vaginal bacterial communities in HIV-infected women using 16S rRNA sequencing and to investigate their association with HPV status. A cross-sectional study was conducted involving 38 HIV-infected women. The study was carried out at the Meru Teaching and Referral Hospital. Dry Evelyn brush self-sampling kit was used forvaginal swab collection. Genomic DNA extraction and amplification were carried out at the Centre for Molecular Biosciences and Genomics (CMB). Bacterial populations were characterized using the 16S rRNA sequencing on an MGI platform. We identified 15,774 reads. Lactobacillus and Gardnerella were the most abundant genera in the study population. Vaginal dysbiosis-associated taxa such as Shuttleworthia and Prevotella were identified among hr-HPV-positive women. Differential abundance analysis revealed an over-representation of the Lactobacillus genus in the hr-HPV positive group. High microbial diversity was observed in both hr-HPV-positive and hr-HPV-negative women. In conclusion, this study highlights the bacterial taxa in the vaginal microbiota and the complex relationship between vaginal microbiome and hr-HPV infections in Kenyan women living with HIV. HIV infection is associated with a more diverse vaginal microbiota; however, the overall composition between the hr-HPV-positive and the hr-HPV-negative women is similar. This could be attributed to HIV infection having already distorted the diversity of the bacterial populations.